The novel provides examples of:

Author Filibuster: The treatment of the conflict between Citizens and Fleshers in the early chapters is so one-sided that one gets the feeling Egan was trying to be the Ayn Rand of the transhumanists, or at least the Bizarro Leiji Matsumoto.

Chekhov's Gun: A sphere becoming a torus in five-dimensional space is the key to unlocking a path to other universes.

Digital Avatar: How Citizens appear to one-another inside their Polises.

Everybody's Dead, Dave: Implied, though not confirmed; the last scene of the novel takes place billions of years after the previous one, Yatima and Paolo have traveled through trillions of alternate universes in pursuit of the Transmuters, and wound up empty-handed. It's unlikely that they'll be able to get back to their home universe, and even if they do, after billions of years, both Yatima and Paolo agree that humanity has almost certainly evolved into something completely unrecognizable, if it even still exists. They talk it over, and make their decisions: Paolo commits suicide, leaving Yatima the last recognizable descendant of the human race. Ve retreats into the Mines, a solipsistic virtual environment where ve will spend the rest of eternity studying mathematics.

A Form You Are Comfortable With: An Inversion is Invoked late in the story. When the Diaspora reaches the second macrosphere, two of the protagonists are approached by something that appears to be Hermann. Which freaks them the hell out, because Hermann didn't come with them. The "Contingency Handler", as it calls itself, explains that it chose this form precisely because it knew that they would know it couldn't actually be Hermann—it's actually a nonsentient AI designed to greet new arrivals in this universe.

Gender-Neutral Writing: Most characters are genderless, and referred to with an invented set of third-person singular pronouns that Egan has also used in his other novels: "Ve" for subjective, "ver" for objective, and "vis" for possessive.

Citizens are digital humans living in a collection of giant virtual reality universes; called Polises. The majority of the novel follows the actions of a small group of Citizens.

Fleshers are biological humans, which include those who evolved naturally from Homo Sapiens (called 'statics') and a multitude of bio-engineered humans; including 'dream apes', which have had conscious thought engineered out of them.

Gleisner Robots are digital humans living in the real world but separate from the fleshers. They inhabit robotic bodies and spend most of their time in space; or daydreaming on the Moon in one case.

Invisible Aliens: Why can't we find any alien races in the Milky Way? They all ran away from the ensuing disaster.

Mary Sue Topia: The Coalition of Polises...rather more like the Classical Greek polises wished they were like than they ever were actually like. A post-cyberpunk Crystal Spires and Togas. An extropian Galt's Gulch. All of the polises seen in the story were clearly designed to provide equal computing resources to all citizens thereof, and the polis hardware is unimpeachable in doing just that.

The Metaverse: Basically what each Polis looks like to its inhabitants.

More Than Three Dimensions: The protagonists discover that subatomic particles actually contain portals to a five-dimensional universe — whose subatomic particles contain portals to another three-dimensional universe, and so on.

Starfish Aliens: Several species are so alien they can only be communicated with through 'bridgers': Citizens who clone themselves repeatedly, with minor alterations in each iteration, until they are themselves utterly alien. Messages are then sent back and forth down the line of clones, each one translating for the next in terms they can understand.

Translation Train Wreck: Yatima finds it very difficult to speak one-to-one with fleshers who have evolved completely alien viewpoints.

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